Np mrd loader

Showing NP-Card for Deoxyuridine (NP0000453)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:38:30 UTC
NP-MRD IDNP0000453
Secondary Accession NumbersNone
Natural Product Identification
Common NameDeoxyuridine
Description2'-Deoxyuridine is a naturally occurring nucleoside. It is similar in chemical structure to uridine, but without the 2'-hydroxyl group. It is considered to be an antimetabolite that is converted to deoxyuridine triphosphate during DNA synthesis. Laboratory suppression of deoxyuridine is used to diagnose megaloblastic anemia due to vitamin B12 and folate deficiencies.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000453 (Deoxyuridine)


  Mrv1652309032023492D          

 16 17  0  0  1  0            999 V2000
   -0.2643   -0.0240    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5252    0.2403    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9062    0.4531    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5046   -0.8239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1431   -0.3089    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6968    1.0436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5756   -0.0377    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3285   -0.8239    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9291   -0.0515    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9784   -1.1190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4761    1.3044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3617    0.2128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8193   -1.4898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0974    0.7552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9693   -0.3432    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8800    1.0126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 11  2  0  0  0  0
  7 12  1  1  0  0  0
  8 13  1  6  0  0  0
  9 14  1  0  0  0  0
 12 15  1  0  0  0  0
 14 16  2  0  0  0  0
  7  8  1  0  0  0  0
 11 14  1  0  0  0  0
M  END
Download

3D MOL for NP0000453 (Deoxyuridine)

HMDB0000012
     RDKit          3D
Deoxyuridine
 28 29  0  0  0  0  0  0  0  0999 V2000
    5.2524   -0.6826   -0.8806 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0283   -0.6077   -0.5872 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3486    0.5620   -0.8323 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0205    0.6356   -0.5112 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4372   -0.4537    0.0355 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0580   -0.4078    0.3798 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3671    0.8672    1.0639 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6884    1.1640    0.3820 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6520    1.5998    1.2869 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0055   -0.1943   -0.1863 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1281   -0.1810   -1.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2888    0.1811   -0.4860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7806   -0.5434   -0.7492 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1244   -1.5875    0.2657 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5242   -2.5864    0.7841 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4177   -1.6748   -0.0413 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8432    1.4284   -1.2752 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4682    1.5403   -0.6940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2071   -1.2470    1.0485 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3534    1.6771    1.0074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6217    0.6782    2.1468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5106    1.9235   -0.4004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4925    2.5912    1.3868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1757   -0.8741    0.6601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2853   -1.2154   -1.5399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9890    0.5125   -2.0019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5840   -0.5299    0.1262 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9000   -2.5753    0.1581 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
  5 14  1  0
 14 15  2  0
 14 16  1  0
 16  2  1  0
 13  6  1  0
  3 17  1  0
  4 18  1  0
  6 19  1  1
  7 20  1  0
  7 21  1  0
  8 22  1  6
  9 23  1  0
 10 24  1  1
 11 25  1  0
 11 26  1  0
 12 27  1  0
 16 28  1  0
M  END
Download

3D SDF for NP0000453 (Deoxyuridine)


  Mrv1652309032023492D          

 16 17  0  0  1  0            999 V2000
   -0.2643   -0.0240    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5252    0.2403    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9062    0.4531    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5046   -0.8239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1431   -0.3089    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6968    1.0436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5756   -0.0377    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3285   -0.8239    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9291   -0.0515    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9784   -1.1190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4761    1.3044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3617    0.2128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8193   -1.4898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0974    0.7552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9693   -0.3432    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8800    1.0126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 11  2  0  0  0  0
  7 12  1  1  0  0  0
  8 13  1  6  0  0  0
  9 14  1  0  0  0  0
 12 15  1  0  0  0  0
 14 16  2  0  0  0  0
  7  8  1  0  0  0  0
 11 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000453

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8+/m0/s1

> <INCHI_KEY>
MXHRCPNRJAMMIM-SHYZEUOFSA-N

> <FORMULA>
C9H12N2O5

> <MOLECULAR_WEIGHT>
228.202

> <EXACT_MASS>
228.074621504

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
21.061427774885466

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-1.49

> <JCHEM_LOGP>
-1.514604078666666

> <ALOGPS_LOGS>
-0.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.907903439872065

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.705729612726527

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9780835884997945

> <JCHEM_POLAR_SURFACE_AREA>
99.1

> <JCHEM_REFRACTIVITY>
51.05490000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.06e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2'-deoxyuridine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000453 (Deoxyuridine)

HMDB0000012
     RDKit          3D
Deoxyuridine
 28 29  0  0  0  0  0  0  0  0999 V2000
    5.2524   -0.6826   -0.8806 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0283   -0.6077   -0.5872 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3486    0.5620   -0.8323 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0205    0.6356   -0.5112 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4372   -0.4537    0.0355 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0580   -0.4078    0.3798 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3671    0.8672    1.0639 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6884    1.1640    0.3820 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6520    1.5998    1.2869 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0055   -0.1943   -0.1863 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1281   -0.1810   -1.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2888    0.1811   -0.4860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7806   -0.5434   -0.7492 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1244   -1.5875    0.2657 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5242   -2.5864    0.7841 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4177   -1.6748   -0.0413 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8432    1.4284   -1.2752 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4682    1.5403   -0.6940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2071   -1.2470    1.0485 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3534    1.6771    1.0074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6217    0.6782    2.1468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5106    1.9235   -0.4004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4925    2.5912    1.3868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1757   -0.8741    0.6601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2853   -1.2154   -1.5399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9890    0.5125   -2.0019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5840   -0.5299    0.1262 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9000   -2.5753    0.1581 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
  5 14  1  0
 14 15  2  0
 14 16  1  0
 16  2  1  0
 13  6  1  0
  3 17  1  0
  4 18  1  0
  6 19  1  1
  7 20  1  0
  7 21  1  0
  8 22  1  6
  9 23  1  0
 10 24  1  1
 11 25  1  0
 11 26  1  0
 12 27  1  0
 16 28  1  0
M  END
Download

PDB for NP0000453 (Deoxyuridine)

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0      -0.493  -0.045   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       0.980   0.449   0.000  0.00  0.00           N+0
HETATM    3  O   UNK     0      -1.692   0.846   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.942  -1.538   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.134  -0.577   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.301   1.948   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.941  -0.070   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.480  -1.538   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.601  -0.096   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       1.826  -2.089   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.755   2.435   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.409   0.397   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -3.396  -2.781   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.915   1.410   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -5.543  -0.641   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       5.376   1.890   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8                                                       
CONECT    5    2    9   10                                                  
CONECT    6    2   11                                                       
CONECT    7    3   12    8                                                  
CONECT    8    4   13    7                                                  
CONECT    9    5   14                                                       
CONECT   10    5                                                            
CONECT   11    6   14                                                       
CONECT   12    7   15                                                       
CONECT   13    8                                                            
CONECT   14    9   16   11                                                  
CONECT   15   12                                                            
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END
Download

3D PDB for NP0000453 (Deoxyuridine)

COMPND    HMDB0000012
HETATM    1  O1  UNL     1       5.252  -0.683  -0.881  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.028  -0.608  -0.587  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.349   0.562  -0.832  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.021   0.636  -0.511  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.437  -0.454   0.036  1.00  0.00           N  
HETATM    6  C4  UNL     1       0.058  -0.408   0.380  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.367   0.867   1.064  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.688   1.164   0.382  1.00  0.00           C  
HETATM    9  O2  UNL     1      -2.652   1.600   1.287  1.00  0.00           O  
HETATM   10  C7  UNL     1      -2.005  -0.194  -0.186  1.00  0.00           C  
HETATM   11  C8  UNL     1      -3.128  -0.181  -1.174  1.00  0.00           C  
HETATM   12  O3  UNL     1      -4.289   0.181  -0.486  1.00  0.00           O  
HETATM   13  O4  UNL     1      -0.781  -0.543  -0.749  1.00  0.00           O  
HETATM   14  C9  UNL     1       2.124  -1.587   0.266  1.00  0.00           C  
HETATM   15  O5  UNL     1       1.524  -2.586   0.784  1.00  0.00           O  
HETATM   16  N2  UNL     1       3.418  -1.675  -0.041  1.00  0.00           N  
HETATM   17  H1  UNL     1       3.843   1.428  -1.275  1.00  0.00           H  
HETATM   18  H2  UNL     1       1.468   1.540  -0.694  1.00  0.00           H  
HETATM   19  H3  UNL     1      -0.207  -1.247   1.049  1.00  0.00           H  
HETATM   20  H4  UNL     1       0.353   1.677   1.007  1.00  0.00           H  
HETATM   21  H5  UNL     1      -0.622   0.678   2.147  1.00  0.00           H  
HETATM   22  H6  UNL     1      -1.511   1.924  -0.400  1.00  0.00           H  
HETATM   23  H7  UNL     1      -2.493   2.591   1.387  1.00  0.00           H  
HETATM   24  H8  UNL     1      -2.176  -0.874   0.660  1.00  0.00           H  
HETATM   25  H9  UNL     1      -3.285  -1.215  -1.540  1.00  0.00           H  
HETATM   26  H10 UNL     1      -2.989   0.513  -2.002  1.00  0.00           H  
HETATM   27  H11 UNL     1      -4.584  -0.530   0.126  1.00  0.00           H  
HETATM   28  H12 UNL     1       3.900  -2.575   0.158  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   16
CONECT    3    4    4   17
CONECT    4    5   18
CONECT    5    6   14
CONECT    6    7   13   19
CONECT    7    8   20   21
CONECT    8    9   10   22
CONECT    9   23
CONECT   10   11   13   24
CONECT   11   12   25   26
CONECT   12   27
CONECT   14   15   15   16
CONECT   16   28
END
Download

SMILES for NP0000453 (Deoxyuridine)

OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O
Download

INCHI for NP0000453 (Deoxyuridine)

InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8+/m0/s1
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View in JSmol
Synonyms
ValueSource
2-DeoxyuridineChEBI
dUChEBI
2'-DeoxyuridineKegg
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-beta-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-beta-delta-ribofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-D-erythro-pentofuranosyl)uracilHMDB
1-(2-Deoxy-delta-erythro-pentofuranosyl)uracilHMDB
2'-DesoxyuridineHMDB
Deoxyribose uracilHMDB
DesoxyuridineHMDB
Uracil deoxyribosideHMDB
Uracil desoxyuridineHMDB
(beta 1-(2-Deoxyribopyranosyl))thymidineHMDB
DeoxyuridineChEBI
Chemical FormulaC9H12N2O5
Average Mass228.2020 Da
Monoisotopic Mass228.07462 Da
IUPAC Name1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name2'-deoxyuridine
CAS Registry Number951-78-0
SMILES
OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O
InChI Identifier
InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8+/m0/s1
InChI KeyMXHRCPNRJAMMIM-SHYZEUOFSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Abelmoschus esculentusFooDB
Actinidia chinensisFooDB
Agaricus bisporusFooDB
AgaveFooDB
Allium ampeloprasumFooDB
Allium ascalonicumFooDB
Allium cepaFooDB
Allium cepa L.FooDB
Allium fistulosumFooDB
Allium sativumFooDB
Allium schoenoprasumFooDB
Allium tuberosumFooDB
Aloysia triphyllaFooDB
AmaranthusFooDB
Amelanchier alnifoliaFooDB
Anacardium occidentaleFooDB
Ananas comosusFooDB
Anas platyrhynchosFooDB
AnatidaeFooDB
Anethum graveolensFooDB
Angelica keiskeiFooDB
Annona cherimolaFooDB
Annona muricataFooDB
Annona reticulataFooDB
Annona squamosaFooDB
Anser anserFooDB
Anthriscus cerefoliumFooDB
Apium graveolensFooDB
Apium graveolens var. dulceFooDB
Apium graveolens var. rapaceumFooDB
Apium graveolens var. secalinumFooDB
Arachis hypogaeaFooDB
Arctium lappaFooDB
Armoracia rusticanaFooDB
Artemisia dracunculusFooDB
Artemisia vulgarisFooDB
Artocarpus altilisFooDB
Artocarpus heterophyllusFooDB
Asparagus officinalisFooDB
Attalea speciosaFooDB
Auricularia auricula-judaeFooDB
Auricularia polytrichaFooDB
Avena sativa L.FooDB
Averrhoa carambolaFooDB
Basella albaFooDB
Benincasa hispidaFooDB
Bertholletia excelsaFooDB
Beta vulgarisFooDB
Beta vulgaris ssp. ciclaFooDB
Biemna ehrenbergiLOTUS Database
Bison bisonFooDB
Borago officinalisFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Brassica alboglabraFooDB
Brassica junceaFooDB
Brassica napusFooDB
Brassica napus var. napusFooDB
Brassica oleraceaFooDB
Brassica oleracea var. botrytisFooDB
Brassica oleracea var. capitataFooDB
Brassica oleracea var. gemmiferaFooDB
Brassica oleracea var. gongylodesFooDB
Brassica oleracea var. italicaFooDB
Brassica oleracea var. sabaudaFooDB
Brassica oleracea var. viridisFooDB
Brassica rapaFooDB
Brassica rapa ssp. chinensisFooDB
Brassica rapa var. pekinensisFooDB
Brassica rapa var. rapaFooDB
Brassica ruvoFooDB
Brosimum alicastrumFooDB
Bubalus bubalisFooDB
Byrsonima crassifoliaFooDB
Cajanus cajanFooDB
Canarium ovatumFooDB
Cannabis sativaCannabisDB
      Not Available
Cantharellus cibariusFooDB
Capparis spinosaFooDB
Capra aegagrus hircusFooDB
Capsicum annuumFooDB
Capsicum annuum L.FooDB
Capsicum annuum var. annuumFooDB
Capsicum chinenseFooDB
Capsicum pubescensFooDB
Carica papaya L.FooDB
Carissa macrocarpaFooDB
Carthamus tinctoriusFooDB
Carum carviFooDB
CaryaFooDB
Carya illinoinensisFooDB
CastaneaFooDB
Castanea crenataFooDB
Castanea mollissimaFooDB
Castanea sativaFooDB
Ceratonia siliquaFooDB
CervidaeFooDB
Cervus canadensisFooDB
Chamaemelum nobileFooDB
Chamerion angustifoliumFooDB
Chara globularisLOTUS Database
Chenopodium albumFooDB
Chenopodium quinoaFooDB
Chrysanthemum coronariumFooDB
Cicer arietinumFooDB
Cichorium endiviaFooDB
Cichorium intybusFooDB
CinnamomumFooDB
Cinnamomum aromaticumFooDB
Cinnamomum verumFooDB
CirsiumFooDB
Citrullus lanatusFooDB
Citrus ×limon (L.) Burm. f. (pro sp.)FooDB
Citrus aurantiifoliaFooDB
Citrus latifoliaFooDB
Citrus limonFooDB
Citrus maximaFooDB
Citrus paradisiFooDB
Citrus reticulataFooDB
Citrus X sinensis (L.) Osbeck (pro. sp.)FooDB
Cocos nuciferaFooDB
Coffea arabica L.FooDB
Coffea canephoraFooDB
Colocasia esculentaFooDB
ColumbaFooDB
ColumbidaeFooDB
Corchorus olitoriusFooDB
Coriandrum sativum L.FooDB
CorylusFooDB
Corylus avellanaFooDB
Crateva religiosaFooDB
Crocus sativusFooDB
Cucumis meloFooDB
Cucumis metuliferusFooDB
Cucumis sativus L.FooDB
CucurbitaFooDB
Cucurbita maximaFooDB
Cucurbita moschataFooDB
Cuminum cyminumFooDB
Curcuma longaFooDB
Cydonia oblongaFooDB
Cymbopogon citratusFooDB
Cynara cardunculusFooDB
Cynara scolymusFooDB
Daucus carotaFooDB
Daucus carota ssp. sativusFooDB
Dimocarpus longanFooDB
DioscoreaFooDB
Dioscorea pentaphyllaFooDB
DiospyrosFooDB
Diospyros kakiFooDB
Diospyros virginianaFooDB
Dromaius novaehollandiaeFooDB
Durio zibethinusFooDB
Dysphania ambrosioidesFooDB
ElaeisFooDB
Eleocharis dulcisFooDB
Elettaria cardamomumFooDB
Empetrum nigrumFooDB
Equus caballusFooDB
Eragrostis tefFooDB
Eriobotrya japonicaFooDB
Eruca vesicaria subsp. SativaFooDB
Eugenia javanicaFooDB
Eugenia unifloraFooDB
Eutrema japonicumFooDB
Fagopyrum esculentumFooDB
Fagopyrum tataricumFooDB
FagusFooDB
Feijoa sellowianaFooDB
Ficus caricaFooDB
Flammulina velutipesFooDB
Foeniculum vulgareFooDB
Fragaria x ananassaFooDB
Gallus gallusFooDB
Garcinia mangostanaFooDB
Gaylussacia baccataFooDB
Ginkgo bilobaFooDB
Glycine maxFooDB
GossypiumFooDB
Grifola frondosaFooDB
Hedysarum alpinumFooDB
Helianthus annuus L.FooDB
Helianthus tuberosusFooDB
Hibiscus sabbariffaFooDB
Hippophae rhamnoidesFooDB
Homo sapiensLOTUS Database
Hordeum vulgareFooDB
Hyssopus officinalis L.FooDB
Illicium verumFooDB
Ipomoea aquaticaFooDB
Ipomoea batatasFooDB
JuglansFooDB
Juglans ailanthifoliaFooDB
Juglans cinereaFooDB
Juglans nigra L.FooDB
Juglans regiaFooDB
Lablab purpureusFooDB
Lactuca sativaFooDB
Lagenaria sicerariaFooDB
Lagopus mutaFooDB
Lathyrus sativusFooDB
Laurus nobilis L.FooDB
Lens culinarisFooDB
Lentinus edodesFooDB
Lepidium sativumFooDB
LeporidaeFooDB
Lepus timidusFooDB
Levisticum officinaleFooDB
Linum usitatissimumFooDB
Litchi chinensisFooDB
Luffa aegyptiacaFooDB
LupinusFooDB
Lupinus albusFooDB
MacadamiaFooDB
Macadamia tetraphyllaFooDB
Malpighia emarginataFooDB
MalusFooDB
Malus pumilaFooDB
Mammea americanaFooDB
Mangifera indicaFooDB
Manihot esculentaFooDB
Manilkara zapotaFooDB
Maranta arundinaceaFooDB
Matricaria recutitaFooDB
Matteuccia struthiopterisFooDB
Medicago sativaFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Melissa officinalis L.FooDB
MenthaFooDB
Mentha aquaticaFooDB
Mentha arvensisFooDB
Mentha spicataFooDB
Mentha x piperitaFooDB
Mespilus germanicaFooDB
Metroxylon saguFooDB
Momordica charantiaFooDB
MorchellaceaeFooDB
Morella rubraFooDB
Moringa oleiferaFooDB
MorusFooDB
Morus nigraFooDB
Mus musculusLOTUS Database
Musa acuminataFooDB
Musa x paradisiacaFooDB
MyricaFooDB
Myristica fragransFooDB
NelumboFooDB
Nelumbo nuciferaFooDB
Nephelium lappaceumFooDB
Numida meleagrisFooDB
Nuphar luteaFooDB
Ocimum basilicumFooDB
OdocoileusFooDB
Oenothera biennisFooDB
Olea europaeaFooDB
OpuntiaFooDB
Opuntia cochenilliferaFooDB
Opuntia macrorhizaFooDB
Origanum majoranaFooDB
Origanum onitesFooDB
Origanum vulgareFooDB
Origanum X majoricumFooDB
OryctolagusFooDB
Oryza rufipogonFooDB
Oryza sativaFooDB
Ovis ariesFooDB
Pachyrhizus erosusFooDB
Panax ginsengFooDB
Pangium eduleFooDB
Panicum miliaceumFooDB
Passiflora edulisFooDB
Pastinaca sativaFooDB
Pediomelum esculentumFooDB
Perideridia oreganaFooDB
Persea americanaFooDB
Petasites japonicusFooDB
Petroselinum crispumFooDB
Phaseolus coccineusFooDB
Phaseolus lunatusFooDB
Phaseolus vulgarisFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Phoenix dactyliferaFooDB
Photinia melanocarpaFooDB
Phyllostachys edulisFooDB
PhysalisFooDB
Physalis philadelphica var. immaculataFooDB
Phytolacca americanaFooDB
Pimenta dioicaFooDB
Pimpinella anisumFooDB
PinusFooDB
Pinus edulisFooDB
Piper nigrum L.FooDB
Pistacia veraFooDB
Pisum sativumFooDB
Pleurotus ostreatusFooDB
Polygonum alpinumFooDB
Portulaca oleraceaFooDB
Pouteria sapotaFooDB
Prunus armeniacaFooDB
Prunus aviumFooDB
Prunus avium L.FooDB
Prunus cerasusFooDB
Prunus domesticaFooDB
Prunus dulcisFooDB
Prunus persicaFooDB
Prunus persica var. nucipersicaFooDB
Prunus persica var. persicaFooDB
Prunus tomentosaFooDB
Prunus virginianaFooDB
Psidium cattleianumFooDB
Psidium guajavaFooDB
Psophocarpus tetragonolobusFooDB
Punica granatumFooDB
Pyrus communisFooDB
Pyrus pyrifoliaFooDB
QuercusFooDB
Raphanus sativusFooDB
Raphanus sativus var. longipinnatusFooDB
Raphanus sativus var. sativusFooDB
Rheum rhabarbarumFooDB
Ribes aureumFooDB
Ribes glandulosumFooDB
Ribes nigrumFooDB
Ribes rubrumFooDB
Ribes uva-crispaFooDB
RosaFooDB
Rubus arcticusFooDB
Rubus chamaemorusFooDB
Rubus idaeusFooDB
Rubus occidentalisFooDB
Rubus spectabilisFooDB
RumexFooDB
Rumex acetosaFooDB
Rumex articusFooDB
Sagittaria latifoliaFooDB
Salix pulchraFooDB
Salvia elegansFooDB
Salvia hispanicaFooDB
Salvia officinalisFooDB
Salvia rosmarinusFooDB
Sambucus nigraFooDB
Sambucus nigra L.FooDB
Satureja hortensis L.FooDB
Satureja montanaFooDB
Scorzonera hispanicaFooDB
Secale cerealeFooDB
Sechium eduleFooDB
Sesamum indicumFooDB
Sesbania bispinosaFooDB
Sinapis albaFooDB
SisymbriumFooDB
Solanum lycopersicumFooDB
Solanum lycopersicum var. cerasiformeFooDB
Solanum lycopersicum var. lycopersicumFooDB
Solanum melongenaFooDB
Solanum quitoenseFooDB
Solanum tuberosumFooDB
Sorbus aucupariaFooDB
Sorghum bicolorFooDB
Spinacia oleraceaFooDB
Spongia sp.-
Struthio camelusFooDB
Stylissa massaLOTUS Database
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Syzygium aromaticumFooDB
Syzygium cuminiFooDB
Syzygium jambosFooDB
Tamarindus indicaFooDB
Taraxacum officinaleFooDB
Tetragonia tetragonioidesFooDB
ThelespermaFooDB
Thymus pulegioidesFooDB
Thymus vulgarisFooDB
Tilia cordataFooDB
Tilia L.FooDB
Tragopogon porrifoliusFooDB
Trigonella foenum-graecumFooDB
TriticumFooDB
Triticum aestivumFooDB
Triticum durumFooDB
Triticum speltaFooDB
Triticum turanicumFooDB
Trypanosoma bruceiLOTUS Database
Typha angustifoliaFooDB
VacciniumFooDB
Vaccinium angustifoliumFooDB
Vaccinium angustifolium X Vaccinium corymbosumFooDB
Vaccinium arboreumFooDB
Vaccinium corymbosumFooDB
Vaccinium deliciosumFooDB
Vaccinium elliottiiFooDB
Vaccinium macrocarponFooDB
Vaccinium myrtilloidesFooDB
Vaccinium myrtillusFooDB
Vaccinium ovalifoliumFooDB
Vaccinium ovatumFooDB
Vaccinium oxycoccosFooDB
Vaccinium parvifoliumFooDB
Vaccinium reticulatumFooDB
Vaccinium stamineumFooDB
Vaccinium uliginosumFooDB
Vaccinium vitis-idaeaFooDB
Valerianella locustaFooDB
VanillaFooDB
Verbena officinalisFooDB
Viburnum eduleFooDB
Vicia fabaFooDB
Vigna aconitifoliaFooDB
Vigna angularisFooDB
Vigna mungoFooDB
Vigna radiataFooDB
Vigna umbellataFooDB
Vigna unguiculataFooDB
Vigna unguiculata ssp. cylindricaFooDB
Vigna unguiculata ssp. unguiculataFooDB
Vigna unguiculata var. sesquipedalisFooDB
VitisFooDB
Vitis aestivalisFooDB
Vitis labruscaFooDB
Vitis rotundifoliaFooDB
Vitis vinifera L.FooDB
Xanthosoma sagittifoliumFooDB
Zea mays L.FooDB
Zingiber officinaleFooDB
ZizaniaFooDB
Zizania aquaticaFooDB
Ziziphus zizyphusFooDB
Species Where Detected
Species NameSourceReference
Escherichia coliKNApSAcK Database
Phakellia mauritianaKNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassPyrimidine 2'-deoxyribonucleosides
Direct ParentPyrimidine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
  • Pyrimidone
  • Hydropyrimidine
  • Pyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Vinylogous amide
  • Lactam
  • Secondary alcohol
  • Urea
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point167 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-1.51Balzarini, J., Matthes, E., Meeus, P., Johns, D. G. & De Clercq, E. (1988) Proceedings of the VI International Symposium on Human Purine and Pyrimidine Metabolism, Hakone, Japan, July 17-21, 1988.
Predicted Properties
PropertyValueSource
Water Solubility90.6 g/LALOGPS
logP-1.5ALOGPS
logP-1.5ChemAxon
logS-0.4ALOGPS
pKa (Strongest Acidic)9.71ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area99.1 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity51.05 m³·mol⁻¹ChemAxon
Polarizability21.06 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000012
DrugBank IDDB02256
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021870
KNApSAcK IDC00019697
Chemspider ID13118
KEGG Compound IDC00526
BioCyc IDDEOXYURIDINE
BiGG ID35251
Wikipedia LinkDeoxyuridine
METLIN ID5086
PubChem Compound13712
PDB IDNot Available
ChEBI ID16450
Good Scents IDNot Available
References
General References
  1. Li KM, Rivory LP, Clarke SJ: Rapid quantitation of plasma 2'-deoxyuridine by high-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry and its application to pharmacodynamic studies in cancer patients. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Jun 5;820(1):121-30. Epub 2005 Apr 19. [PubMed:15866500 ]
  2. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  3. Di Stefano G, Busi C, Derenzini M, Trere D, Fiume L: Conjugation of 5-fluoro-2'-deoxyuridine with lactosaminated poly-l-lysine to reduce extrahepatic toxicity in the treatment of hepatocarcinomas. Ital J Gastroenterol Hepatol. 1998 Apr;30(2):173-7. [PubMed:9675653 ]
  4. Reidy JA: Deoxyuridine increases folate-sensitive fragile site expression in human lymphocytes. Am J Med Genet. 1987 Jan;26(1):1-5. [PubMed:3812550 ]
  5. Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7. [PubMed:6656991 ]
  6. Huong PL, Kolk AH, Eggelte TA, Verstijnen CP, Gilis H, Hendriks JT: Measurement of antigen specific lymphocyte proliferation using 5-bromo-deoxyuridine incorporation. An easy and low cost alternative to radioactive thymidine incorporation. J Immunol Methods. 1991 Jul 5;140(2):243-8. [PubMed:1906076 ]
  7. Kanazawa S, Herbert V: Detection of folate deficiency in alcoholism using the peripheral blood lymphocyte deoxyuridine suppression test. J Nutr Sci Vitaminol (Tokyo). 1986 Jun;32(3):251-7. [PubMed:3761048 ]
  8. Zittoun J, Zittoun R: Modern clinical testing strategies in cobalamin and folate deficiency. Semin Hematol. 1999 Jan;36(1):35-46. [PubMed:9930567 ]
  9. Fairbanks LD, Marinaki AM, Carrey EA, Hammans SR, Duley JA: Deoxyuridine accumulation in urine in thymidine phosphorylase deficiency (MNGIE). J Inherit Metab Dis. 2002 Nov;25(7):603-4. [PubMed:12638947 ]
  10. Remacha A, Barcelo MJ, Pastor M, Ubeda J, Espadaler M, Gimferrer E: The deoxyuridine suppression test in peripheral lymphocytes. Eur J Haematol. 1990 Mar;44(3):196-200. [PubMed:2328792 ]
  11. Galanis E, Goldberg R, Reid J, Atherton P, Sloan J, Pitot H, Rubin J, Adjei AA, Burch P, Safgren SL, Witzig TE, Ames MM, Erlichman C: Phase I trial of sequential administration of raltitrexed (Tomudex) and 5-iodo-2'-deoxyuridine (IdUrd). Ann Oncol. 2001 May;12(5):701-7. [PubMed:11432631 ]
  12. (). Akhrem, A.A. et al., Org. Magn. Reson., 1979, 12, 247, (cmr). .
  13. (). Fox, J.J. et al., Adv. Carbohydr. Chem., 1959, 14, 283, (rev). .
  14. (). Rimerman, R.A. et al., J. Chromatogr., B: Biomed. Appl., 1993, 619, 29-35, (5'-triphosphate). .
  15. (). Schinazi, R.F. et al., J. Med. Chem., 1978, 21, 1141, (synth, acid). .
  16. (). Barr, P.J. et al., Tetrahedron, 1980, 36, 1269, (cryst struct). .
  17. (). Ludwig, J. et al., Synthesis, 1982, 32-34, (5'-phosphate). .
  18. (). Dematte, N. et al., Comp. Biochem. Physiol., B: Comp. Biochem., 1986, 84, 11, (isol, acid). .
  19. (). Rahman, A. et al., Acta Cryst. B, 1972, 28, 2260, (cryst struct). .
  20. (). Sakema, S. et al., Comp. Biochem. Physiol., B: Comp. Biochem., 1985, 82, 107-109, (isol). .
  21. (). Aldrich Library of FT-IR Spectra, 1st edn., 1985, 2, 816A, (ir). .
  22. (). Kikugawa, K. et al., Chem. Pharm. Bull., 1969, 17, 785, (synth, deriv). .
  23. (). Sprecher, C.A. et al., Biopolymers, 1977, 16, 2243, (cd). .
  24. (). Komori, T. et al., Annalen, 1980, 653-668, (isol). .
  25. (). Aldrich Library of 13C and 1H FT NMR Spectra, 1992, 3, 374B, (nmr). .
  26. (). Hruska, F.E. et al., Can. J. Chem., 1974, 52, 497, (conformn, pmr). .
  27. (). U.S. Pat., 1966, 3 280 104, CA, 66, 38207y. .
  28. (). Lidgren, G. et al., J. Nat. Prod., 1988, 51, 1277-1280, (2'-Deoxy-3-methyluridine). .